When Washingtonian magazine polled congressional aides on the "best and worst" of Congress, Thomas was voted #2 for "brainiest", #3 for "workhorse", and #1 for "meanest" and overwhelmingly for "hottest temper" in the House.[1] Thomas is known for being able to comprehend and communicate the intricacies of obscure legislative matters, studying testimony and research reports himself instead of relying on executive summaries from his aides. Thomas is also known for losing his temper when people are unprepared, earning a reputation for sharp interrogations. "He's revered, but he's also reviled to some degree", fellow representative Mark Foley told CQ Weekly.

On March 6, 2006, Thomas announced he would not seek reelection, retiring after 28 years in the House. A major influence on his decision was the internal GOP term limits that would require him to relinquish his Ways and Means chairmanship even if he were re-elected.[citation needed] Thomas endorsed a former aide, Assemblyman Kevin McCarthy, who was elected to replace him.

In the 1992 Rubbergate banking scandal, involving House members writing checks when the funds were not available, Bill Thomas bounced 119 checks, the tenth-highest amount for a Republican member of Congress.[4][unreliable source?].

The Bakersfield Californian published an article on Thomas about an affair with Deborah Steelman,[5] a lobbyist for Cigna, Pfizer, Aetna, United Healthcare Corporation, the Healthcare Leadership Council, and Prudential. Thomas was then chair of the House subcommittee that regulates HMOs. "Any personal failures of commitment or responsibility to my wife, family or friends are just that, personal," the former congressman wrote in an "open letter to friends and neighbors." Neither he nor Deborah Steelman explicitly denied the allegations. Deborah Steelman was promoted to VP of Eli Lilly, steered huge campaign gifts to Thomas's war chest and the health care industry scored big with the passage of the Medicare Modernization Act of 2003.

In July 2003, Thomas called the U.S. Capitol Police to eject Democrats from a meeting room. A few days later, he tearfully apologized on the House floor for what he called his "just plain stupid" decision to ask the police to eject the Congressmen.[6][7]